|
| Status |
Public on Nov 19, 2009 |
| Title |
MSC Suz12 ChIP-chip |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
MSC Suz12 ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hESc-derived mesenchymal stem cell
sample type: hESc-derived mesenchymal stem cells, Suz12 ChIP
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were either pretreated with detergent for pre-extraction of proteins from the chromatin or directly crosslinked with 1% formaldehyde for 10 min at room temperature. The ChIP protocol by Agilent was followed. After purification, the DNA was amplified with the Whole Genome Amplification Kit (Sigma) for 2 rounds.
|
| Label |
Cy5
|
| Label protocol |
Standard Nimblegen ChIP labelling protocol
|
| |
|
| Channel 2 |
| Source name |
MSC Input chromatin
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hESc-derived mesenchymal stem cell
sample type: hESc-derived mesenchymal stem cells, input chromatin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were either pretreated with detergent for pre-extraction of proteins from the chromatin or directly crosslinked with 1% formaldehyde for 10 min at room temperature. The ChIP protocol by Agilent was followed. After purification, the DNA was amplified with the Whole Genome Amplification Kit (Sigma) for 2 rounds.
|
| Label |
Cy3
|
| Label protocol |
Standard Nimblegen ChIP labelling protocol
|
| |
|
| |
| Hybridization protocol |
Standard Nimblegen Hybridization protocol
|
| Scan protocol |
Standard Nimblegen Scan protocol
|
| Description |
hESc-derived mesenchymal stem cells, Suz12 ChIP
|
| Data processing |
Calculated log2 intensity ratios from raw intensity values
|
| |
|
| Submission date |
Nov 16, 2009 |
| Last update date |
Nov 18, 2009 |
| Contact name |
Peter Kharchenko |
| Organization name |
Harvard Medical School
|
| Department |
DBMI
|
| Lab |
Kharchenko
|
| Street address |
10 Shattuck St.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL9673 |
| Series (1) |
| GSE19046 |
A Region of Human HoxD that Confers Polycomb-Group Responsiveness |
|
